But LE has been around for a while and its certs mostly work fine everywhere! That's partially because it was already in a ton of root programs, and partially because of cross-signed roots. A cross-signed root is effectively the root CA except signed by a different CA. A client that doesn't trust the new root yet trusts it via the cros-signed root.
Most sites need 2 certificates in the chain to be validated: the leaf certificate certifying the site itself and the intermediate online CA that signs leaf certs. The intermediate is signed by the root, which is in your trust store so you don't need to send it. Lots of sites send it anyway. This is a misconfiguration and just serves to make TLS connections slower: you're sending an extra certificate along that by definition nobody uses. This is because it's self-signed: you either already trusted it anyway (and then didn't need it) or you don't trust it and then the self-signed certificate is unconvincing.
New CAs also need their cross signed root sent along to be widely supported, so they basically get that worse performance all the time. Unfortunately, you don't know in advance which roots a TLS client will trust, so until you're in every major trust store, you have to. Now that LE is in every major trust store, it's a real first-class CA and everyone gets to look forward to doing away with the cross-signed root crutch. (You can't do it immediately because old, unpatched machines.)
LE is great and has done wonders to make all the other CAs up their game.
You can read more about LE's trust chain here: https://letsencrypt.org/certificates/